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1 function [UNIQUE_NEW_EXONS, GRAPHNODES, ORDER_OF_GRAPHNODE, EIRS_IN_SEQ] = transform_single_end_reads(gene, SEQUENCED_LENGTH)
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2 % This function calculates all regions onto which a read may fall.
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3 % SEQUENCED_LENGTH is the length of a read.
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4
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5 SPLICINGEVENTS=gene.splicingevents;
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6 SEQUENCE=gene.sequence;
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7 EXONSEQUENCE=gene.exonsequence;
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8
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9 NB_OF_TRANS = size(EXONSEQUENCE,1);
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10
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11 NEWEXONS = 1:(length(SPLICINGEVENTS) - 1);
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12 UNIQUE_NEW_EXONS = NEWEXONS(SEQUENCE>0);
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13
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14 NB_OF_EXONS = length(UNIQUE_NEW_EXONS);
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15 MAX_EXON_NB_TO_POS = cumsum((NEWEXONS .* SEQUENCE) > 0);
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16
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17 % NB_EXONSEQUENCE is for each transcript the position in
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18 % SPLICINGEVENTS where one of its exonic region starts and 0 if it
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19 % is intronic
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20
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21 NB_EXONSEQUENCE = EXONSEQUENCE .* repmat(NEWEXONS,NB_OF_TRANS,1);
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22
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23 %%% This contains all exons
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24 GRAPHNODES = [];
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25
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26 %%% This is the array where a 1 is in column j if that EIR (Exons in
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27 %a region covered by a read) is contained in the transcript
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28 EIRS_IN_SEQ = [];
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29
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30 CURRENT_NODE = 0;% To catch errors with non-initalized variable
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31
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32 EIR_TRANSCRIPTS = cell(1,NB_OF_TRANS);
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33 ORDER_OF_GRAPHNODE = cell(1,NB_OF_TRANS);
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34 LENGTHS_OF_GRAPHNODE = cell(1,NB_OF_TRANS);
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35
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36 SPLICING_LENGTHS = SPLICINGEVENTS(2:end) - SPLICINGEVENTS(1:end-1);
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37
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38 for i = 1:NB_OF_TRANS
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39
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40 %%% remove zero positions, adjust splicing positions
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41 CURRENT_EXONS = NB_EXONSEQUENCE(i, EXONSEQUENCE(i,:) > 0);
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42
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43 SPLICING_CORRECT = cumsum(SPLICING_LENGTHS .* (NB_EXONSEQUENCE(i,:) == 0));
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44 %SPLICING_CORRECT contains the position of SPLICINGSEQUENCE in
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45 %the transcript when all introns are spliced out
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46 SPLICING_CORRECT = [1, SPLICINGEVENTS(2:end) - SPLICING_CORRECT];
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47
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48 %This ensures that the end of the transcript is also in CURRENT_SPLICINGEVENTS
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49 IDX = EXONSEQUENCE(i,:) == 1 ;
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50 IDX(find(EXONSEQUENCE(i,:) == 1, 1, 'last') + 1) = true;
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51 CURRENT_SPLICINGEVENTS = SPLICING_CORRECT(IDX);
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52 if length(CURRENT_SPLICINGEVENTS) == 0
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53 continue
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54 end
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55 LASTPOS = CURRENT_SPLICINGEVENTS(end);
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56 if LASTPOS <= SEQUENCED_LENGTH
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57 warning('CURRENT_SPLICINGEVENTS(end) > SEQUENCED_LENGTH')
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58 end
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59 %assert(LASTPOS > SEQUENCED_LENGTH,'CURRENT_SPLICINGEVENTS(end) > SEQUENCED_LENGTH')
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60 % Calculate the positions when the EIRS can change
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61
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62 % Determine positions which start SEQUENCED_LENGTH positions before a splicing event
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63 % defines a window of size SEQUENCED_LENGTH around the CURRENT_SPLICINGEVENTS
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64 READEVENTS_START = max([CURRENT_SPLICINGEVENTS(1:end - 1) - SEQUENCED_LENGTH + 1; ones(1,length(CURRENT_SPLICINGEVENTS)-1)],[],1);
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65 READEVENTS_END = min([CURRENT_SPLICINGEVENTS(2:end); repmat(LASTPOS - SEQUENCED_LENGTH,1,length(CURRENT_SPLICINGEVENTS(2:end)))],[],1);
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66
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67 % Calculate EIRS
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68 % CHANGE_POINTS are those points in a transcript where a EIR changes, namly the splicesites of that transcript plus and
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69 % minus the SEQUENCED_LENGTH - the above descibed window
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70 CHANGE_POINTS = unique([READEVENTS_START, READEVENTS_END]);
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71
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72 for j = 1:(length(CHANGE_POINTS) - 1)
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73
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74 POINTS_OF_INTEREST = ( READEVENTS_START(1,:) <= CHANGE_POINTS(j)) & (READEVENTS_END(1,:) > CHANGE_POINTS(j));
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75
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76 % MAX_EXON_NB_TO_POS is mapping back to the unspliced coordinates
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77 CURRENT_EIRS = zeros(1,NB_OF_EXONS);
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78 CURRENT_EIRS( MAX_EXON_NB_TO_POS(CURRENT_EXONS(POINTS_OF_INTEREST))) = 1;
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79
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80 %%% Already seen such exon composition in sliding
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81 %%% window?
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82 [TEMP, CURRENT_NODE] = intersect(GRAPHNODES, CURRENT_EIRS, 'rows');
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83 if isempty(TEMP)
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84 GRAPHNODES = [GRAPHNODES; CURRENT_EIRS]; %Add Key
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85 EIRS_IN_SEQ = [EIRS_IN_SEQ, zeros(NB_OF_TRANS,1)];
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86 CURRENT_NODE = size(GRAPHNODES,1);
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87 end
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88
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89 EIRS_IN_SEQ(i,CURRENT_NODE) = 1;
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90 ORDER_OF_GRAPHNODE{i} = [ORDER_OF_GRAPHNODE{i}, CURRENT_NODE];
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91 LENGTHS_OF_GRAPHNODE{i} = [LENGTHS_OF_GRAPHNODE{i}, [CHANGE_POINTS(j); CHANGE_POINTS(j+1)]];
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92 end
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93 end
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94 |
